2PD3 | pdb_00002pd3

Crystal Structure of the Helicobacter pylori Enoyl-Acyl Carrier Protein Reductase in Complex with Hydroxydiphenyl Ether Compounds, Triclosan and Diclosan

PDB DOI: https://doi.org/10.2210/pdb2PD3/pdb
Entry: 2PD3 supersedes: 1JVF

Classification: OXIDOREDUCTASE
Organism(s): Helicobacter pylori
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-03-31 Released: 2007-04-17
Deposition Author(s): Lee, H.H., Moon, J.H., Suh, S.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.259 (Depositor), 0.258 (DCC)
R-Value Work:
0.233 (Depositor), 0.231 (DCC)
R-Value Observed:
0.233 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of the Helicobacter pylori enoyl-acyl carrier protein reductase in complex with hydroxydiphenyl ether compounds, triclosan and diclosan

Lee, H.H., Moon, J.H., Suh, S.W.

(2007) Proteins 69: 691-694

PubMed: 17879346 Search on PubMed
DOI: https://doi.org/10.1002/prot.21586
Primary Citation Related Structures:
2PD3, 2PD4

Organizational Affiliation

Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Korea.

Macromolecule Content

Total Structure Weight: 123.88 kDa
Atom Count: 8,866
Modeled Residue Count: 1,096
Deposited Residue Count: 1,100
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-[acyl-carrier-protein] reductase [NADH]	A, B, C, D	275	Helicobacter pylori	Mutation(s): 0 EC: 1.3.1.9
UniProt
Find proteins for O24990 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O24990 Go to UniProtKB: O24990
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O24990
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
TCL Query on TCL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	TRICLOSAN C₁₂ H₇ Cl₃ O₂ XEFQLINVKFYRCS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.259 (Depositor), 0.258 (DCC)
R-Value Work: 0.233 (Depositor), 0.231 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.353	α = 90
b = 94.911	β = 106.21
c = 75.376	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-04-17

Deposition Author(s):

Lee, H.H.

Moon, J.H.

Suh, S.W.

This entry supersedes: 1JVF

Revision History (Full details and data files)

Version 1.0: 2007-04-17
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description